{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T20:37:47Z","timestamp":1771101467995,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1411,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Novel technologies brought in unprecedented amounts of high-throughput sequencing data along with great challenges in their analysis and interpretation. The percent-spliced-in (PSI, ) metric estimates the incidence of single-exon\u2013skipping events and can be computed directly by counting reads that align to known or predicted splice junctions. However, the majority of human splicing events are more complex than single-exon skipping.<\/jats:p>\n               <jats:p>Results: In this short report, we present a framework that generalizes the metric to arbitrary classes of splicing events. We change the view from exon centric to intron centric and split the value of into two indices, and , measuring the rate of splicing at the 5\u2032 and 3\u2032 end of the intron, respectively. The advantage of having two separate indices is that they deconvolute two distinct elementary acts of the splicing reaction. The completeness of splicing index is decomposed in a similar way. This framework is implemented as bam2ssj, a BAM-file\u2013processing pipeline for strand-specific counting of reads that align to splice junctions or overlap with splice sites. It can be used as a consistent protocol for quantifying splice junctions from RNA-seq data because no such standard procedure currently exists.<\/jats:p>\n               <jats:p>Availability: The C code of bam2ssj is open source and is available at https:\/\/github.com\/pervouchine\/bam2ssj<\/jats:p>\n               <jats:p>Contact: \u00a0dp@crg.eu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts678","type":"journal-article","created":{"date-parts":[[2012,11,23]],"date-time":"2012-11-23T03:52:09Z","timestamp":1353642729000},"page":"273-274","source":"Crossref","is-referenced-by-count":98,"title":["Intron-centric estimation of alternative splicing from RNA-seq data"],"prefix":"10.1093","volume":"29","author":[{"given":"Dmitri D.","family":"Pervouchine","sequence":"first","affiliation":[{"name":"1 Centre de Regulaci\u00f3 Gen\u00f2mica (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and 3Moscow State University, 119992 Moscow, Russia"},{"name":"1 Centre de Regulaci\u00f3 Gen\u00f2mica (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and 3Moscow State University, 119992 Moscow, Russia"},{"name":"1 Centre de Regulaci\u00f3 Gen\u00f2mica (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and 3Moscow State University, 119992 Moscow, Russia"}]},{"given":"David G.","family":"Knowles","sequence":"additional","affiliation":[{"name":"1 Centre de Regulaci\u00f3 Gen\u00f2mica (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and 3Moscow State University, 119992 Moscow, Russia"},{"name":"1 Centre de Regulaci\u00f3 Gen\u00f2mica (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and 3Moscow State University, 119992 Moscow, Russia"}]},{"given":"Roderic","family":"Guig\u00f3","sequence":"additional","affiliation":[{"name":"1 Centre de Regulaci\u00f3 Gen\u00f2mica (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and 3Moscow State University, 119992 Moscow, Russia"},{"name":"1 Centre de Regulaci\u00f3 Gen\u00f2mica (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and 3Moscow State University, 119992 Moscow, Russia"}]}],"member":"286","published-online":{"date-parts":[[2012,11,21]]},"reference":[{"key":"2023012810215258100_bts678-B1","doi-asserted-by":"crossref","first-page":"S11","DOI":"10.1186\/1471-2105-13-S6-S11","article-title":"Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data","volume":"13","author":"Kakaradov","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023012810215258100_bts678-B2","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1038\/nmeth.1528","article-title":"Analysis and design of RNA sequencing experiments for identifying isoform regulation","volume":"7","author":"Katz","year":"2010","journal-title":"Nat. Methods"},{"key":"2023012810215258100_bts678-B3","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012810215258100_bts678-B4","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1038\/nature08903","article-title":"Transcriptome genetics using second generation sequencing in a Caucasian population","volume":"464","author":"Montgomery","year":"2010","journal-title":"Nature"},{"key":"2023012810215258100_bts678-B5","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1038\/ng.259","article-title":"Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing","volume":"40","author":"Pan","year":"2008","journal-title":"Nat. Genet."},{"key":"2023012810215258100_bts678-B6","doi-asserted-by":"crossref","first-page":"1616","DOI":"10.1101\/gr.134445.111","article-title":"Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs","volume":"22","author":"Tilgner","year":"2012","journal-title":"Genome Res."},{"key":"2023012810215258100_bts678-B7","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nprot.2012.016","article-title":"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks","volume":"7","author":"Trapnell","year":"2012","journal-title":"Nat. Protoc."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/2\/273\/48890359\/bioinformatics_29_2_273.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/2\/273\/48890359\/bioinformatics_29_2_273.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T11:51:37Z","timestamp":1674906697000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/2\/273\/203629"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,11,21]]},"references-count":7,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2013,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts678","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,1,15]]},"published":{"date-parts":[[2012,11,21]]}}}